More Like this

1. Seasonality of the Microbial Community Composition in the North Atlantic

   https://doi.org/10.3389/fmars.2021.624164  

   Bolaños, Luis M. ; Choi, Chang Jae ; Worden, Alexandra Z. ; Baetge, Nicholas ; Carlson, Craig A. ; Giovannoni, Stephen ( February 2021 , Frontiers in Marine Science)

   null (Ed.)

   Planktonic communities constitute the basis of life in marine environments and have profound impacts in geochemical cycles. In the North Atlantic, seasonality drives annual transitions in the ecology of the water column. Phytoplankton bloom annually in spring as a result of these transitions, creating one of the major biological pulses in productivity on earth. The timing and geographical distribution of the spring bloom as well as the resulting biomass accumulation have largely been studied using the global capacity of satellite imaging. However, fine-scale variability in the taxonomic composition, spatial distribution, seasonal shifts, and ecological interactions with heterotrophic bacterioplankton has remained largely uncharacterized. The North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) conducted four meridional transects to characterize plankton ecosystems in the context of the annual bloom cycle. Using 16S rRNA gene-based community profiles we analyzed the temporal and spatial variation in plankton communities. Seasonality in phytoplankton and bacterioplankton composition was apparent throughout the water column, with changes dependent on the hydrographic origin. From winter to spring in the subtropic and subpolar subregions, phytoplankton shifted from the predominance of cyanobacteria and picoeukaryotic green algae to diverse photosynthetic eukaryotes. By autumn, the subtropics were dominated by cyanobacteria, while a diverse array of eukaryotes dominated the subpolar subregions. Bacterioplankton were also strongly influenced by geographical subregions. SAR11, the most abundant bacteria in the surface ocean, displayed higher richness in the subtropics than the subpolar subregions. SAR11 subclades were differentially distributed between the two subregions. Subclades Ia.1 and Ia.3 co-occurred in the subpolar subregion, while Ia.1 dominated the subtropics. In the subtropical subregion during the winter, the relative abundance of SAR11 subclades “II” and 1c.1 were elevated in the upper mesopelagic. In the winter, SAR202 subclades generally prevalent in the bathypelagic were also dominant members in the upper mesopelagic zones. Co-varying network analysis confirmed the large-scale geographical organization of the plankton communities and provided insights into the vertical distribution of bacterioplankton. This study represents the most comprehensive survey of microbial profiles in the western North Atlantic to date, revealing stark seasonal differences in composition and richness delimited by the biogeographical distribution of the planktonic communities. 

   more » « less
2. Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling

   https://doi.org/10.1038/s41396-018-0169-y  

   Needham, David M. ; Fichot, Erin B. ; Wang, Ellice ; Berdjeb, Lyria ; Cram, Jacob A. ; Fichot, Cédric G. ; Fuhrman, Jed A. ( June 2018 , The ISME Journal)

   Short timescale observations are valuable for understanding microbial ecological processes. We assessed dynamics in relative abundance and potential activities by sequencing the small sub-unit ribosomal RNA gene (rRNA gene) and rRNA molecules (rRNA) of Bacteria, Archaea, and Eukaryota once to twice daily between March 2014 and May 2014 from the surface ocean off Catalina Island, California. Typically Ostreococcus, Braarudosphaera, Teleaulax, and Synechococcus dominated phytoplankton sequences (including chloroplasts) while SAR11, Sulfitobacter, and Fluviicola dominated non-phytoplankton Bacteria and Archaea. We observed short-lived increases of diatoms, mostly Pseudo-nitzschia and Chaetoceros, with quickly responding Bacteria and Archaea including Flavobacteriaceae (Polaribacter & Formosa), Roseovarius, and Euryarchaeota (MGII), notably the exact amplicon sequence variants we observed responding similarly to another diatom bloom nearby, 3 years prior. We observed correlations representing known interactions among abundant phytoplankton rRNA sequences, demonstrating the biogeochemical and ecological relevance of such interactions: (1) The kleptochloroplastidic ciliate Mesodinium 18S rRNA gene sequences and a single Teleaulax taxon (via 16S rRNA gene sequences) were correlated (Spearman r = 0.83) yet uncorrelated to a Teleaulax 18S rRNA gene OTU, or any other taxon (consistent with a kleptochloroplastidic or karyokleptic relationship) and (2) the photosynthetic prymnesiophyte Braarudosphaera bigelowii and two strains of diazotrophic cyanobacterium UCYN-A were correlated and each taxon was also correlated to other taxa, including B. bigelowii to a verrucomicrobium and a dictyochophyte phytoplankter (all r > 0.8). We also report strong correlations (r > 0.7) between various ciliates, bacteria, and phytoplankton, suggesting interactions via currently unknown mechanisms. These data reiterate the utility of high-frequency time series to show rapid microbial reactions to stimuli, and provide new information about in situ dynamics of previously recognized and hypothesized interactions.

    

   more » « less
3. Sulfur isotope fractionations constrain the biological cycling of dimethylsulfoniopropionate in the upper ocean

   https://doi.org/10.1002/lno.11901  

   Osorio‐Rodriguez, Daniela ; Razo‐Mejia, Manuel ; Dalleska, Nathan F. ; Sessions, Alex L. ; Orphan, Victoria J. ; Adkins, Jess F. ( July 2021 , Limnology and Oceanography)

   The rapid turnover of dimethylsulfoniopropionate (DMSP), likely the most relevant dissolved organic sulfur compound in the surface ocean, makes it pivotal to understand the cycling of organic sulfur. Dimethylsulfoniopropionate is mainly synthesized by phytoplankton, and it can be utilized as carbon and sulfur sources by marine bacteria or cleaved by bacteria or algae to produce the volatile compound dimethylsulfide (DMS), involved in the formation of sulfate aerosols. The fluxes between the consumption (i.e., demethylation) and cleavage pathways are thought to depend on community interactions and their sulfur demand. However, a quantitative assessment of the sulfur partitioning between each of these pathways is still missing. Here, we report for the first time the sulfur isotope fractionations by enzymes involved in DMSP degradation with different catalytic mechanisms, expressed heterologously inEscherichia coli. We show that the residual DMSP from the demethylation pathway is 2.7‰ enriched inδ³⁴S relative to the initial DMSP, and that the fractionation factor (³⁴ε) of the cleavage pathways varies between −1 and −9‰. The incorporation of these fractionation factors into mass balance calculations constrains the biological fates of DMSP in seawater, supports the notion that demethylation dominates over cleavage in marine environments, and could be used as a proxy for the dominant pathways of degradation of DMSP by marine microbial communities.

    

   more » « less
4. The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points

   https://doi.org/10.1007/s00248-022-01969-y  

   Doane, Michael P. ; Johnson, Colton J. ; Johri, Shaili ; Kerr, Emma N. ; Morris, Megan M. ; Desantiago, Ric ; Turnlund, Abigail C. ; Goodman, Asha ; Mora, Maria ; Lima, Laís Farias Oliveira ; et al ( February 2022 , Microbial Ecology)

   The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of theTriakis semifasciata(leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray–Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, includingPseudomonas,Erythrobacter,Alcanivorax,Marinobacter, andSphingopxisbeing consistently abundant across time-points, whileLimnobacterandXyellaexhibited switching patterns with high relative abundance in 2013,SphingobiumandSphingomonain 2015, andAltermonas,Leeuwenhoekiella,Gramella, andMaribacterin 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray–Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.

    

   more » « less
5. Sulfur metabolites that facilitate oceanic phytoplankton–bacteria carbon flux

   https://doi.org/10.1038/s41396-019-0455-3  

   Landa, Marine ; Burns, Andrew S. ; Durham, Bryndan P. ; Esson, Kaitlin ; Nowinski, Brent ; Sharma, Shalabh ; Vorobev, Alexey ; Nielsen, Torben ; Kiene, Ronald P. ; Moran, Mary Ann ( June 2019 , The ISME Journal)

   Unlike biologically available nitrogen and phosphorus, which are often at limiting concentrations in surface seawater, sulfur in the form of sulfate is plentiful and not considered to constrain marine microbial activity. Nonetheless, in a model system in which a marine bacterium obtains all of its carbon from co-cultured phytoplankton, bacterial gene expression suggests that at least seven dissolved organic sulfur (DOS) metabolites support bacterial heterotrophy. These labile exometabolites of marine dinoflagellates and diatoms include taurine, N-acetyltaurine, isethionate, choline-O-sulfate, cysteate, 2,3-dihydroxypropane-1-sulfonate (DHPS), and dimethylsulfoniopropionate (DMSP). Leveraging from the compounds identified in this model system, we assessed the role of sulfur metabolites in the ocean carbon cycle by mining the Tara Oceans dataset for diagnostic genes. In the 1.4 million bacterial genome equivalents surveyed, estimates of the frequency of genomes harboring the capability for DOS metabolite utilization ranged broadly, from only 1 out of every 190 genomes (for the C2 sulfonate isethionate) to 1 out of every 5 (for the sulfonium compound DMSP). Bacteria able to participate in DOS transformations are dominated by Alphaproteobacteria in the surface ocean, but by SAR324, Acidimicrobiia, and Gammaproteobacteria at mesopelagic depths, where the capability for utilization occurs in higher frequency than in surface bacteria for more than half the sulfur metabolites. The discovery of an abundant and diverse suite of marine bacteria with the genetic capacity for DOS transformation argues for an important role for sulfur metabolites in the pelagic ocean carbon cycle.

    

   more » « less